X-26637619-C-T

Variant names:

• chrX-26637619-C-T
• rs1558145
• ENST00000674719.1:n.622+75020C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000674719.1(VENTXP1):​n.622+75020C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 111,473 control chromosomes in the GnomAD database, including 773 homozygotes. There are 3,802 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (773 hom., 3802 hem., cov: 23)
• Consequence: VENTXP1 ENST00000674719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

Genes affected

VENTXP1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674719.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VENTXP1	ENST00000674719.1		n.622+75020C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 12043 AN: 111424 Hom.: 773 Cov.: 23

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0975

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.135

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 12048 AN: 111473 Hom.: 773 Cov.: 23 AF XY: 0.113 AC XY: 3802 AN XY: 33727

African (AFR) AF: 0.0804 AC: 2475 AN: 30775

American (AMR) AF: 0.307 AC: 3208 AN: 10446

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 286 AN: 2638

East Asian (EAS) AF: 0.401 AC: 1399 AN: 3489

South Asian (SAS) AF: 0.250 AC: 668 AN: 2672

European-Finnish (FIN) AF: 0.0352 AC: 212 AN: 6025

Middle Eastern (MID) AF: 0.102 AC: 22 AN: 215

European-Non Finnish (NFE) AF: 0.0660 AC: 3497 AN: 53004

Other (OTH) AF: 0.132 AC: 202 AN: 1526

Alfa AF: 0.0849 Hom.: 3510

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1558145; hg19: chrX-26655736;